Biofilm metagenome
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR067873.fastq.gz | Fastqsanger.gz | |||
| DRR067874.fastq.gz | Fastqsanger.gz | |||
| DRR067875.fastq.gz | Fastqsanger.gz | |||
| DRR067876.fastq.gz | Fastqsanger.gz | |||
| DRR067877.fastq.gz | Fastqsanger.gz |
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Project description:GOAL: Identification of genes and/or pathways involved in the pathogenesis of animal models of Rheumatoid Arthritis (RA). Total RNA samples were extracted from synovial fibroblast ex vivo cultures or whole joints (J), isolated from arthritic mice (197, DARE) and their corresponding normal (F1, wt) littermates. Fluorescent-labeled cRNA probes were utilized to hybridize (in duplicates for 197, indicated by "new") the Affymetrix Mu11K oligonucleotide DNA chipset (A+B). In detail the samples are:<br> <table> <tr> <td> <u>Animal model</u> </td> <td> <u>Sample source</u> </td> <td> <u>Sample name</u> </td> </tr> <tr> <td> Tg197 </td> <td> Tg197 ex-vivo cultured synoviocyte populations </td> <td> 197 </td> </tr> <tr> <td> Tg197 </td> <td> Tg197 ex-vivo cultured synoviocyte populations </td> <td> 197new </td> </tr> <tr> <td> Tg197 </td> <td> wt ex-vivo cultured synoviocyte populations </td> <td> F1 </td> </tr> <tr> <td> Tg197 </td> <td> wt ex-vivo cultured synoviocyte populations </td> <td> F1new </td> </tr> <tr> </tr> <tr> <td> Tg197 </td> <td> Tg197 whole joints </td> <td> 197J </td> </tr> <tr> <td> Tg197 </td> <td> Tg197 whole joints </td> <td> 197Jnew </td> </tr> <tr> <td> Tg197 </td> <td> wt whole joints </td> <td> F1J </td> </tr> <tr> <td> Tg197 </td> <td> wt whole joints </td> <td> F1Jnew </td> </tr> <tr> </tr> <tr> <td> DARE </td> <td> DARE ex-vivo cultured synoviocyte populations </td> <td> DARE </td> </tr> <tr> <td> DARE </td> <td> wt ex-vivo cultured synoviocyte populations </td> <td> wt </td> </tr> <tr> <td> DARE </td> <td> DARE whole joints </td> <td> DAREJ </td> </tr> <tr> <td> DARE </td> <td> wt whole joints </td> <td> wtJ </td> </tr> </table> <br> Submitted files carry the extension A or B, corresponding to the subArrays of chipset Mu11K. Arthritic samples were always compared with the corresponding wt sample and not to a common reference chip.
2005-06-30 | E-MEXP-255 | biostudies-arrayexpress
Project description:UBTF tandem duplications (TD) have recently emerged as a subtype-defining alteration in pediatric acute myeloid leukemia (pAML), which is characterized by HOXB gene dysregulation and a poor response to conventional chemotherapy. Here, we use protein-protein interaction studies to show that UBTF-TD maintains interactions with components of the RNA pol I complex, while also engaging with a network of unique protein interactors specific to UBTF-TD, like KMT2A. These data suggest that UBTF- TD both preserves canonical UBTF functions and demonstrates gain of function activities. Furthermore, we show that UBTF-TD and KMT2A co-localize to key genomic targets dysregulated in UBTF-TD myeloid malignancies, like HOXB gene clusters and MEIS1. Using a protein degradation system, we show that stemness, proliferation, and the HOXB molecular signature are dependent on sustained UBTF-TD localization to chromatin. Finally, we show UBTF-TD leukemias are sensitive to menin inhibition—providing a viable therapeutic strategy for children with this high-risk AML subtype.
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Project description:UBTF tandem duplications (UBTF-TD) define a high-risk molecular subtype of acute myeloid leukemia (AML) characterized by poor clinical outcomes. While menin inhibitors have shown therapeutic promise, acquired resistance remains a significant challenge. Here, we use proteomic, genomic, and functional analyses to uncover mechanisms underlying UBTF-TD mediated leukemogenesis. We show that TDs create nuclear export signal (NES) motifs, which mediate interactions with Exportin-1 (XPO1) and chromatin-associated partners. These interactions drive aberrant chromatin binding and transcriptional activation of genes commonly dysregulated in UBTF-TD tumors, including the HOXA/HOXB clusters. We demonstrate that these NES motifs are critical for mislocalization of UBTF-TD proteins, cellular transformation, and transcriptional dysregulation. Importantly, we identify the XPO1 inhibitor eltanexor as a potential therapeutic strategy. Eltanexor treatment disrupts UBTF-TD chromatin localization, reduces tumor burden, and promotes differentiation in preclinical models. These findings provide mechanistic insights into UBTF-TD-driven leukemogenesis and highlight XPO1 inhibition as a promising therapy for UBTF-TD AMLs.
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Project description:UBTF tandem duplications (TD) have recently emerged as a subtype-defining alteration in pediatric AML (pAML), which is characterized by HOXB gene dysregulation and a poor response to conventional chemotherapy. Here, we use protein-protein interaction studies to show that UBTF-TD maintains interactions with components of the RNA pol I complex, while also engaging with a network of unique protein interactors specific to UBTF-TD, like KMT2A. These data suggest that UBTF-TD both preserves canonical UBTF functions and demonstrates gain of function activities. Furthermore, we show that UBTF-TD and KMT2A co-localize to key genomic targets dysregulated in UBTF-TD leukemias, like HOXB gene clusters and MEIS1. Using a protein degradation system, we show that stemness, proliferation, and the HOXB molecular signature are dependent on sustained UBTF-TD localization to chromatin. Finally, we show UBTF-TD leukemias are sensitive to menin inhibition—providing a viable therapeutic strategy for children with this high-risk AML subtype
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